The Rapidly Expanding Field of “–Omics” Technologies - Science For Environmental Protection: The Road Ahead - page 204

PROTEOMICS
Proteomics is the study of the entire complement of proteins in a cell or
tissue—the proteome. The proteome is much more complicated than the genome
because the proteome differs from cell to cell and from time to time, whereas the
genome of an organism is largely unchanged between cells and over time. Fur-
thermore, most proteins in a cell undergo posttranslational modifications (for
example, phosphorylation, glycosylation, methylation, and ubiquination), which
can result in several functional forms of the same protein. The proteome is po-
tentially far more informative than the genome with respect to environmental
response. Measuring and understanding changes in the proteome after environ-
mental perturbations are therefore increasingly important in many fields of envi-
ronmental science and engineering. Proteomic technologies and approaches will
have an increasingly important role in environmental monitoring and health risk
assessment of relevance to EPA. For example, proteome-based biomarkers may
be useful in deciphering the associations between pesticide exposure and cancer
and will perhaps lead to potential predictive biomarkers of pesticide-induced
carcinogenesis (George and Shukla 2011).
Proteomics has been used to explore “a multitude of bacterial processes,
ranging from the analysis of environmental communities [and the] identification
of virulence factors to the proteome-guided optimization of production strains”
(Chao and Hansmeier 2012). Proteomics has become a valuable tool for the
global analysis of bacterial physiology and pathogenicity, although many chal-
lenges remain, especially in the accurate prediction of phenotypic consequences
based on a given proteome composition (Chao and Heinsmeyer 2012). Lemos et
al. (2010) have discussed the advantages of and challenges to using proteomics
in ecosystems research.
METABOLOMICS
Substantial improvements in instrumentation, especially nuclear magnetic
resonance spectroscopy (Serkova and Niemann 2006) and mass spectrometry
(Dettmer et al. 2007), provide increasingly sensitive approaches to measuring
hundreds or even thousands of small molecules in a cell in a matter of minutes.
The new technologies have given rise to a promising new -omics technology
referred to as metabolomics—the "systematic study of the unique chemical fin-
gerprints that specific cellular processes leave behind" (Bennett 2005) or, more
specifically, the study of their small-molecule metabolite profiles. “In analogy to
the genome, which is used as synonym for the entirety of all genetic informa-
tion, the metabolome represents the entirety of the metabolites within a biologi-
cal system” (Oldiges et al. 2007). The total number of metabolites in a single
cell, tissue, or organism is, of course, highly variable and depends on the bio-
logic system investigated. Hundreds of distinct metabolites have been identified
in microorganisms. For example, the Escherichia coli database EcoCYC con-
tains over 2,000 metabolite entries (Keseler et al. 2011), and the metabolome of